Pranabesh,
you do not need to modify the parameter files in any way, if you use
multiple instances of the same newly defined entity in your system: If
you have several Mn ions in your structure, it is sufficient to load the
*definition* of that ion via your parameter files. leap will use that
definition for every residue and atoms defined therein; it does not
matter that the coordinates in the parameter files do not match those
from your input (as is normally the case for the standard amino acid
parameters when loading a protein structure into leap).
However, if your structure contains not just several isolated Mn2+
centers but an Mn-cluster with bonds, angle and torsional terms, the
parameter files are not sufficient. New parameter definitions are
needed, and this is far beyond the beginner's level.
Thus, if your structure contains several isolated Mn2+ ions, try out the
original/unmodified parameter files.
If your structure contains an Mn-cluster, you cannot simply use those
parameters.
Hope that helps.
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 01/07/2022 06:18 AM, Pranabesh Mandal (PhD, Bioinformatics
August-2019) wrote:
> Dear Anselm,
> I tried to set up the simulation with one MN and it is not giving any error
> message. But when I tried this with four MN and with modified metals.prp
> (added 3 more MN with coordinates) then it showed multiple errors (asking
> for bond and torsion parameters). You can find my tleap input and errors
> below.
>
> tleap input: tleap.in
> set default PBRadii mbondi2
> source leaprc.protein.ff14SB
> source leaprc.gaff2
> loadoff ions94.lib
> loadamberparams frcmod.ionsjc_tip3p
> loadamberparams frcmod.vdWall
> loadamberparams frcmod.constph
> source leaprc.water.tip3p
> loadAmberParams metals.dat
> loadAmberPrep metals.prp
> x = loadPDB new.pdb
> saveAmberParm x stp_gas.parm7 stp_gas.rst7
> savePdb x amb.pdb
> solvatebox x TIP3PBOX 8
> addions x NA 0
> saveAmberParm x stp_wat.parm7 stp_wat.rst7
> charge x
> quit
>
> *erros:*
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
> Building angle parameters.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find angle parameter: MN - MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find angle parameter: MN - MN - MN
> Building proper torsion parameters.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> ** No torsion terms for MN-MN-MN-MN
> Building improper torsion parameters.
> total 788 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> Parameter file was not saved.
> Writing pdb file: amb.pdb
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> Converting N-terminal residue name to PDB format: NMET -> MET
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> Converting C-terminal residue name to PDB format: CGLY -> GLY
> Solute vdw bounding box: 48.251 123.586 209.116
> Total bounding box for atom centers: 64.251 139.586 225.116
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 67.185 142.904 227.880 angstroms.
> Volume: 2187880.029 A^3
> Total mass 1150956.598 amu, Density 0.874 g/cc
> Added 62336 residues.
> 5 NA ions required to neutralize.
> Adding 5 counter ions to "x" using 1A grid
> Grid extends from solute vdw + 1.37 to 7.37
> Resolution: 1.00 Angstrom.
> Solvent present: replacing closest with ion
> when steric overlaps occur
> Calculating grid charges
> (No solvent overlap)
> Placed NA in x at (-0.04, 38.58, 89.76).
> (Replacing solvent molecule)
> Placed NA in x at (-2.56, 36.54, 93.22).
> (No solvent overlap)
> Placed NA in x at (-11.04, 24.58, 64.76).
> (No solvent overlap)
> Placed NA in x at (-23.04, 33.58, 76.76).
> (No solvent overlap)
> Placed NA in x at (0.96, 30.58, 89.76).
>
> Done adding ions.
> Checking Unit.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> There is a bond of 6.785308 angstroms between:
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> There is a bond of 7.211941 angstroms between:
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> There is a bond of 5.920439 angstroms between:
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Note.
> Ignoring the warnings from Unit Checking.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find bond parameter for: MN - MN
> Building angle parameters.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find angle parameter: MN - MN - MN
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> Could not find angle parameter: MN - MN - MN
> Building proper torsion parameters.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Error!
> ** No torsion terms for MN-MN-MN-MN
> Building improper torsion parameters.
> total 788 improper torsions applied
> Building H-Bond parameters.
> Incorporating Non-Bonded adjustments.
>
> /home/dvsingh/softwares/amber18/bin/teLeap: Warning!
> Parameter file was not saved.
> Total unperturbed charge: -0.000000
> Total perturbed charge: -0.000000
> Quit
>
> Exiting LEaP: Errors = 12; Warnings = 18; Notes = 3.
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Received on Thu Jan 06 2022 - 23:30:02 PST
